unable to find genes when export to SPRING object

[MichaelPeibo]

Hi scanpy team, I convert Seurat obj to anndata with: mda_ad <- Convert(from = mda, to = "anndata",filename = 'mda_day27_ad.h5ad')

mda_ad AnnData object with n_obs × n_vars = 6039 × 19331 obs: 'n_genes', 'n_counts', 'orig_ident', 'percent_mito', 'S_Score', 'G2M_Score', 'Phase', 'old_ident', 'res_1_2' var: 'gene.mean', 'gene.dispersion', 'gene.dispersion.scaled' obsm: 'X_pca', 'X_tsne'

Then I run as scanpy's tutorial https://github.com/theislab/scanpy_usage/blob/master/171111_SPRING_export/SPRING_export.ipynb to export SPRING, however, I was unable to find no response when I enter a gene in the web browser. I have all required files in the folder.

Any suggestion how to solve it?

Thanks!

[falexwolf]

I fear you have to address the Spring authors directly, @swolock, for instance, who wrote the exporter.

If it continues to be buggy, you might also look at cellxgene, which is very professionally developed and directly reads in Scanpy's h5ad files.

[swolock]

Hi @MichaelPeibo,

It's possible there's an unknown SPRING bug behind your issue, in which case the easiest way for me to help would be for you to share your SPRING folder with me (if this is possible). But before doing that, answers to the following questions might help me narrow it down:

• Can you confirm you're using Python 2 to start the local server?
• Would you mind sharing the output from the console/terminal that is running the server?
• What is the exact URL you entered?

And @falexwolf -- thanks for referring the issue to me!

[MichaelPeibo]

Hi @falexwolf Thanks for pointing it out.

Hi @swolock I went through it today. I guess it may be due to the multiple web server error when I first start it?

Or maybe both my server and me need a rest and restart.....

Sorry to bother, very nice interactive tool!!!

[MichaelPeibo]

@falexwolf @swolock
Hi, I recheck my web history, I doubted that it is due to old springViewer I used. I followed this tutorial https://github.com/theislab/scanpy_usage/blob/master/171111_SPRING_export/SPRING_export.ipynb and it gave the link : http://localhost:8000//springViewer.html?

However, I got through it with http://localhost:8000/springViewer_1_6_dev.html?